iiinova — where your digital self keeps evolving

Reposted by Cécile Tran Kiem

IDDjobs @iddjobs.org · 25/09/2026

Postdoc (London, UK) Develop new methods for pathogen genomic epidemiology with @ceciletk.bsky.social at Imperial College London @mrc-outbreak.bsky.social More details: iddjobs.org/jobs/2596

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

This has been a really fun project to work on! Many thanks to Katie Kistler, @ryanhisner.bsky.social, Trevor Bedford, everyone who generated the underlying sequences and the team behind the Viridian project (tinyurl.com/viridian-paper) for making such a high-quality resource available! 5/

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

We also explored how often such events showed evidence of between-host transmission and the mutation patterns associated with onward spread. While we didn’t find evidence for transmission in most events, branches that did spread tended to carry mutations also found in successful clades. 4/

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

Saltational-like branches carry a distinct mutational signature, enriched in Spike mutations particularly in the receptor-binding domain. This signature quantitatively matches that of persistent human infections, confirming the role of chronic infections as a major source for such events. 3/

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

We systematically investigated saltational evolution, developing a scalable approach to detect long branches with evidence for positive selection in a SARS-CoV-2 phylogeny of 4.4M high-quality genomes. We identified 1576 saltational-like branches across every year and nearly every region sampled. 2/

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026

The emergence and spread of highly mutated variants have shaped the COVID-19 pandemic. In our new work (tinyurl.com/ncov-saltati...), we find that such jumps aren’t rare anomalies but a recurring feature of SARS-CoV-2 evolution, occurring at low but detectable rates over time & across geographies.

tinyurl.com

SARS-CoV-2 saltational events are recurrent and trace to persistent human infections

SARS-CoV-2 evolution is characterized by gradual mutation accumulation but has been punctuated by rare yet impactful highly mutated variants. Whether such saltational jumps are a broad feature of SARS...

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Cécile Tran Kiem @ceciletk.bsky.social · 19/03/2026

Excited to share our work w/ @justinlessler.bsky.social, Trevor Bedford & Amanda Perofsky: doi.org/10.1098/rspb.... We investigate when sequence datasets are informative about between-group transmission, and how this depends on the relative pace of mutation, between-group transmission and sampling.

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

This work could not have been possible without many people, including Trevor Bedford, Amanda Perofsky and @paredesmig.bsky.social, and all the hard work at @doh.wa.gov, @brotmanbaty.bsky.social and UW Virology to build a genomic sentinel SARS-CoV-2 surveillance with detailed linked metadata! 7/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

Finally, building on the expectation that infectors should tend to be observed first within pairs of identical sequences, we use the timing of sequence collection to understand the groups driving transmission. 6/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

Patterns of occurrence of identical sequences between age groups show assortativity in age mixing and transmission between generations. Jointly analyzing the ages & geographies of pairs of identical sequences, we find that age transmission patterns vary across spatial scales. 5/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

The location of pairs of identical sequences is in line with expectations from cell phone derived mobility data. Outliers in the relationship between genetic and mobility data can be explained by large clusters of identical sequences shared between male prisons' postal codes. 4/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

Applying the framework to more than 114,000 SARS-CoV-2 sequences collected through genomic sentinel surveillance in WA, USA between Mar 2021 & Dec 2022, we find a strong signal for local spread, with identical sequences having an increased risk of being observed between nearby counties. 3/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

Genetic proximity between infecting viruses indicates epidemiological linkage. Here, we introduce a relative risk (RR) metric that quantifies how the number of pairs of identical sequences in two groups differs from what we expect from the sequencing effort. 2/

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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025

Pathogen genomes can provide insights into underlying disease transmission patterns but new methods are needed to analyze large genome datasets. Our work using identical pathogen sequences to characterize fine scale SARS-CoV-2 transmission was just published in @nature.com tinyurl.com/bdzk9xjj 🥳

tinyurl.com

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences - Nature

The analysis of pairs of identical SARS-CoV-2 genome sequences enables characterization of transmission patterns between geographies and age groups.

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